Would mounting my amp on the same side I mount my woofers cause any problems? I mean that would be the strongest part of the box considering its a double baffle?

There's enough space to fit it there so I don't see how it would be a problem but figured I'd post to get input, any possible side affects?

As long as you put some sort of vibrating suppression under the amp then it's fine by me.

I use 34" thick foam under my amp's mounting feet whenever i need to install it on a panel that will be flexing.

Make sure you compensate for the screw length because of the padding.